As said above, finding and capturing the legendaries should be as challenging as possible. The challenges should be tricky, but not completely unsolvable as that might deter people who dislike puzzles from finding and catching the legendary.

The locations and when the legendaries are able to be captured should be near the end of the game when the true purpose of what the legendaries resemble are clearly known. I'm sure there will be a perfect time and a perfect place.

As for capturing the legendary, the capture rate should be of normal legendary capture rates; not too easy but also not exceedingly difficult. A couple of Dusk Balls or Ultra Balls should be able to do the trick.